derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

Author
Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Date of publication
None
Maintainer
Leonardo Collado-Torres <lcollado@jhu.edu>
License
Artistic-2.0
Version
1.8.0
URLs

View on Bioconductor

Man pages

analyzeChr
Run the derfinder analysis on a chromosome
annotateRegions
Assign genomic states to regions
calculatePvalues
Calculate p-values and identify regions
calculateStats
Calculate F-statistics at base pair resolution from a loaded...
coerceGR
Coerce the coverage to a GRanges object for a given sample
collapseFullCoverage
Collapse full coverage information for efficient quantile...
coverageToExon
Extract coverage information for exons
createBw
Export coverage to BigWig files
createBwSample
Create a BigWig file with the coverage information for a...
define_cluster
Define a cluster to use.
derfinder-deprecated
Deprecated functions in package 'derfinder'
derfinder-package
Annotation-agnostic differential expression analysis of...
extendedMapSeqlevels
Change naming style for a set of sequence names
filterData
Filter the positions of interest
findRegions
Find non-zero regions in a Rle
fullCoverage
Load the unfiltered coverage information from a group of BAM...
genomeData
Genome samples processed data
genomeDataRaw
Genome samples processed data
genomeFstats
F-statistics for the example data
genomeInfo
Genome samples information
genomeRegions
Candidate DERs for example data
genomicState
Genomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverage
Extract coverage information for a set of regions
getTotalMapped
Calculate the total number of mapped reads
loadCoverage
Load the coverage information from a group of BAM files
makeGenomicState
Obtain the genomic state per region from annotation
makeModels
Build model matrices for differential expression
mergeResults
Merge results from different chromosomes
preprocessCoverage
Transform and split the data
railMatrix
Identify regions data by a coverage filter and get a count...
rawFiles
Construct full paths to a group of raw input files
regionMatrix
Identify regions data by a coverage filter and get a count...
sampleDepth
Calculate adjustments for library size

Files in this package

derfinder/DESCRIPTION
derfinder/NAMESPACE
derfinder/NEWS
derfinder/R
derfinder/R/Deprecated.R
derfinder/R/analyzeChr.R
derfinder/R/annotateRegions.R
derfinder/R/calculatePvalues.R
derfinder/R/calculateStats.R
derfinder/R/coerceGR.R
derfinder/R/collapseFullCoverage.R
derfinder/R/coverageToExon.R
derfinder/R/createBw.R
derfinder/R/createBwSample.R
derfinder/R/define_cluster.R
derfinder/R/derfinder-package.R
derfinder/R/extendedMapSeqlevels.R
derfinder/R/filterData.R
derfinder/R/findRegions.R
derfinder/R/fullCoverage.R
derfinder/R/genomeData-data.R
derfinder/R/genomeDataRaw-data.R
derfinder/R/genomeFstats-data.R
derfinder/R/genomeInfo-data.R
derfinder/R/genomeRegions-data.R
derfinder/R/genomicState-data.R
derfinder/R/getRegionCoverage.R
derfinder/R/getTotalMapped.R
derfinder/R/loadCoverage.R
derfinder/R/makeGenomicState.R
derfinder/R/makeModels.R
derfinder/R/mergeResults.R
derfinder/R/preprocessCoverage.R
derfinder/R/railMatrix.R
derfinder/R/rawFiles.R
derfinder/R/regionMatrix.R
derfinder/R/sampleDepth.R
derfinder/R/utils.R
derfinder/README.md
derfinder/build
derfinder/build/vignette.rds
derfinder/data
derfinder/data/genomeData.RData
derfinder/data/genomeDataRaw.RData
derfinder/data/genomeFstats.RData
derfinder/data/genomeInfo.RData
derfinder/data/genomeRegions.RData
derfinder/data/genomicState.RData
derfinder/inst
derfinder/inst/CITATION
derfinder/inst/doc
derfinder/inst/doc/derfinder-quickstart.R
derfinder/inst/doc/derfinder-quickstart.Rmd
derfinder/inst/doc/derfinder-quickstart.html
derfinder/inst/doc/derfinder-users-guide.R
derfinder/inst/doc/derfinder-users-guide.Rmd
derfinder/inst/doc/derfinder-users-guide.html
derfinder/inst/extdata
derfinder/inst/extdata/chr21
derfinder/inst/extdata/chr21/annotation.Rdata
derfinder/inst/extdata/chr21/coveragePrep.Rdata
derfinder/inst/extdata/chr21/fstats.Rdata
derfinder/inst/extdata/chr21/optionsStats.Rdata
derfinder/inst/extdata/chr21/regions.Rdata
derfinder/inst/extdata/chr21/timeinfo.Rdata
derfinder/inst/extdata/genomeData
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai
derfinder/man
derfinder/man/analyzeChr.Rd
derfinder/man/annotateRegions.Rd
derfinder/man/calculatePvalues.Rd
derfinder/man/calculateStats.Rd
derfinder/man/coerceGR.Rd
derfinder/man/collapseFullCoverage.Rd
derfinder/man/coverageToExon.Rd
derfinder/man/createBw.Rd
derfinder/man/createBwSample.Rd
derfinder/man/define_cluster.Rd
derfinder/man/derfinder-deprecated.Rd
derfinder/man/derfinder-package.Rd
derfinder/man/extendedMapSeqlevels.Rd
derfinder/man/filterData.Rd
derfinder/man/findRegions.Rd
derfinder/man/fullCoverage.Rd
derfinder/man/genomeData.Rd
derfinder/man/genomeDataRaw.Rd
derfinder/man/genomeFstats.Rd
derfinder/man/genomeInfo.Rd
derfinder/man/genomeRegions.Rd
derfinder/man/genomicState.Rd
derfinder/man/getRegionCoverage.Rd
derfinder/man/getTotalMapped.Rd
derfinder/man/loadCoverage.Rd
derfinder/man/makeGenomicState.Rd
derfinder/man/makeModels.Rd
derfinder/man/mergeResults.Rd
derfinder/man/preprocessCoverage.Rd
derfinder/man/railMatrix.Rd
derfinder/man/rawFiles.Rd
derfinder/man/regionMatrix.Rd
derfinder/man/sampleDepth.Rd
derfinder/tests
derfinder/tests/test-all.R
derfinder/tests/testthat
derfinder/tests/testthat/test_ER_level.R
derfinder/tests/testthat/test_Fstats.R
derfinder/tests/testthat/test_annotation.R
derfinder/tests/testthat/test_data.R
derfinder/tests/testthat/test_findRegions.R
derfinder/tests/testthat/test_misc.R
derfinder/vignettes
derfinder/vignettes/derfinder-quickstart.Rmd
derfinder/vignettes/derfinder-users-guide.Rmd